Repbase Reports

2001, Volume 1, Issue 3
March 31, 2001
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 4

ATCOPIA78_I

Internal portion of the ATCOPIA78 copia-like LTR-retrotransposon - a consensus sequence.

Submitted:
31-Mar-2001
Accepted:
31-Mar-2001
Key Words:
LTR-retrotransposon; COPIA superfamily; ATCOPIA78 family; internal region; pol; reverse transcriptase; ATCOPIA78LTR; ATCOPIA78_I
Source:
consensus
Organism:
Arabidopsis thaliana
Taxonomy:
Eukaryota; Viridiplantae; Charophyta/Embryophyta group; Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; Rosidae; Capparales; Brassicaceae; Arabidopsis
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Internal portion of the ATCOPIA78 copia-like LTR-retrotransposon.
Journal:
Repbase Reports 1:(3) p. 4 (2001)
Abstract:
ATCOPIA78_I is a consensus sequence of an internal region of ATCOPIA78 copia-like retroelement flanked by ~1% divergent LTRs, ATCOPIA78LTR, and 5 bp-long target-site duplicates. ATCOPIA78 is one of ~100 families of copia-like LTR-retrotransposons, which were active in the A. thaliana genome during last 20 Myrs. The consensus sequence has been reconstructed based on eight copies present in the genome. These copies are ~99.4% identical to the consensus sequence. ATCOPIA78_I encodes ATCOPIA78p, a 1352-aa copia-like polyprotein. ATCOPIA78p: MASNNVPFQVPVLTKSNYDNWSLRMKAILGAHDVWEIVEKGFIEPENEGSLSQTQKDGLRDSRKRDKKAL CLIYQGLDEDTFEKVVEATSAKEAWEKLRTSYKGADQVKKVRLQTLRGEFEALQMKEGELVSDYFSRVLT VTNNLKRNGEKLDDVRIMEKVLRSLDLKFEHIVTVIEETKDLEAMTIEQLLGSLQAYEEKKKKKEDIVEQ VLNMQITKEENGQSYQRRGGGQVRGRGRGGYGNGRGWRPHEDNTNQRGENSSRGRGKGHPKSRYDKSSVK CYNCGKFGHYASECKAPSNKKFEEKANYVEEKIQEEDMLLMASYKKDEQEENHKWYLDSGASNHMCGRKS MFAELDESVRGNVALGDESKMEVKGKGNILIRLKNGDHQFISNVYYIPSMKTNILSLGQLLEKGYDIRLK DNNLSIRDQESNLITKVPMSKNRMFVLNIRNDIAQCLKMCYKEESWLWHLRFGHLNFGGLELLSRKEMVR GLPCINHPNQVCEGCLLGKQFKMSFPKESSSRAQKPLELIHTDVCGPIKPKSLGKSNYFLLFIDDFSRKT WVYFLKEKSEVFEIFKKFKAHVEKESGLVIKTMRSDRGGEFTSKEFLKYCEDNGIRRQLTVPRSPQQNGV AERKNRTILEMARSMLKSKRLPKELWAEAVACAVYLLNRSPTKSVSGKTPQEAWSGRKPGVSHLRVFGSI AHAHVPDEKRSKLDDKSEKYIFIGYDNNSKGYKLYNPDTKKTIISRNIVFDEEGEWDWNSNEEDYNFFPH FEEDEPEPTREEPPSEEPTTPPTSPTSSQIEESSSERTPRFRSIQELYEVTENQENLTLFCLFAECEPMD FQEAIEKKTWRNAMDEEIKSIQKNDTWELTSLPNGHKAIGVKWVYKAKKNSKGEVERYKARLVAKGYSQR AGIDYDEVFAPVARLETVRLIISLAAQNKWKIHQMDVKSAFLNGDLEEEVYIEQPQGYIVKGEEDKVLRL KKALYGLKQAPRAWNTRIDKYFKEKDFIKCPYEHALYIKIQKEDILIACLYVDDLIFTGNNPSMFEEFKK EMTKEFEMTDIGLMSYYLGIEVKQEDNGIFITQEGYAKEVLKKFKMDDSNPVCTPMECGIKLSKKEEGEG VDPTTFKSLVGSLRYLTCTRPDILYAVGVVSRYMEHPTTTHFKAAKRILRYIKGTVNFGLHYSTTSDYKL VGYSDSDWGGDVDDRKSTSGFVFYIGDTAFTWMSKKQPIVTLSTCEAEYVAATSCVCHAIWLRNLLKELS LPQEEPTKIFVDNKSAIALAKNPVFHDRSKHIDTRYHYIRECVSKKDVQLEYVKTHDQVADIFTKPLKRE DFIKMRSLLGVAKSSLRGGVES It's possible that some copies of ATCOPIA78 are still active retrotransposons.
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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